Well it is really, they've played the majority of the Premiership games, and on top of that in the Europa League that team yesterday played extra games;
Mark Schwarzer - 17
Paul Konchesky - 12 (injured)
Aaron Hughes - 16
Brede Hangeland - 15
Chris Baird - 15
Simon Davies - 10 (injured)
Danny Murphy - 12 (injured)
Dickson Etuhu - 13 (injured)
Damien Duff - 13 (injured)
Zoltan Gera - 17
Bobby Zamora - 16
That is a lot of extra games (don't forget FA was up to a replay of the Quarter Final, and another replay too iirc and the League Cup). Although yesterday can partly be blamed for tiredness, but the overall higher skill level of Atletico prevailed.